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1.

Dynamic trans-acting factor colocalization in human cells.

Xie, Dan; Boyle, Alan P; Wu, Linfeng; Zhai, Jie; Kawli, Trupti; Snyder, Michael.

Cell; 155(3): 713-24, 2013 Oct 24.

Artículo en Inglés | MEDLINE | ID: mdl-24243024

2.

Personal omics profiling reveals dynamic molecular and medical phenotypes.

Chen, Rui; Mias, George I; Li-Pook-Than, Jennifer; Jiang, Lihua; Lam, Hugo Y K; Chen, Rong; Miriami, Elana; Karczewski, Konrad J; Hariharan, Manoj; Dewey, Frederick E; Cheng, Yong; Clark, Michael J; Im, Hogune; Habegger, Lukas; Balasubramanian, Suganthi; O'Huallachain, Maeve; Dudley, Joel T; Hillenmeyer, Sara; Haraksingh, Rajini; Sharon, Donald; Euskirchen, Ghia; Lacroute, Phil; Bettinger, Keith; Boyle, Alan P; Kasowski, Maya; Grubert, Fabian; Seki, Scott; Garcia, Marco; Whirl-Carrillo, Michelle; Gallardo, Mercedes; Blasco, Maria A; Greenberg, Peter L; Snyder, Phyllis; Klein, Teri E; Altman, Russ B; Butte, Atul J; Ashley, Euan A; Gerstein, Mark; Nadeau, Kari C; Tang, Hua; Snyder, Michael.

Cell; 148(6): 1293-307, 2012 Mar 16.

Artículo en Inglés | MEDLINE | ID: mdl-22424236

3.

Multiplexed long-read plasmid validation and analysis using OnRamp.

Mumm, Camille; Drexel, Melissa L; McDonald, Torrin L; Diehl, Adam G; Switzenberg, Jessica A; Boyle, Alan P.

Genome Res; 33(5): 741-749, 2023 May.

Artículo en Inglés | MEDLINE | ID: mdl-37156622

4.

Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.

Dong, Shengcheng; Boyle, Alan P.

Nucleic Acids Res; 50(1): e6, 2022 01 11.

Artículo en Inglés | MEDLINE | ID: mdl-34648033

5.

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.

Ouyang, Ningxin; Boyle, Alan P.

Genome Res; 30(7): 1040-1046, 2020 07.

Artículo en Inglés | MEDLINE | ID: mdl-32660981

6.

High-resolution mapping and characterization of open chromatin across the genome.

Boyle, Alan P; Davis, Sean; Shulha, Hennady P; Meltzer, Paul; Margulies, Elliott H; Weng, Zhiping; Furey, Terrence S; Crawford, Gregory E.

Cell; 132(2): 311-22, 2008 Jan 25.

Artículo en Inglés | MEDLINE | ID: mdl-18243105

7.

Broad noncoding transcription suggests genome surveillance by RNA polymerase V.

Tsuzuki, Masayuki; Sethuraman, Shriya; Coke, Adriana N; Rothi, M Hafiz; Boyle, Alan P; Wierzbicki, Andrzej T.

Proc Natl Acad Sci U S A; 117(48): 30799-30804, 2020 12 01.

Artículo en Inglés | MEDLINE | ID: mdl-33199612

8.

SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.

Nishizaki, Sierra S; Boyle, Alan P.

BMC Bioinformatics; 23(1): 317, 2022 Aug 04.

Artículo en Inglés | MEDLINE | ID: mdl-35927613

9.

Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.

Nielsen, Jonas B; Fritsche, Lars G; Zhou, Wei; Teslovich, Tanya M; Holmen, Oddgeir L; Gustafsson, Stefan; Gabrielsen, Maiken E; Schmidt, Ellen M; Beaumont, Robin; Wolford, Brooke N; Lin, Maoxuan; Brummett, Chad M; Preuss, Michael H; Refsgaard, Lena; Bottinger, Erwin P; Graham, Sarah E; Surakka, Ida; Chu, Yunhan; Skogholt, Anne Heidi; Dalen, Håvard; Boyle, Alan P; Oral, Hakan; Herron, Todd J; Kitzman, Jacob; Jalife, José; Svendsen, Jesper H; Olesen, Morten S; Njølstad, Inger; Løchen, Maja-Lisa; Baras, Aris; Gottesman, Omri; Marcketta, Anthony; O'Dushlaine, Colm; Ritchie, Marylyn D; Wilsgaard, Tom; Loos, Ruth J F; Frayling, Timothy M; Boehnke, Michael; Ingelsson, Erik; Carey, David J; Dewey, Frederick E; Kang, Hyun M; Abecasis, Gonçalo R; Hveem, Kristian; Willer, Cristen J.

Am J Hum Genet; 102(1): 103-115, 2018 01 04.

Artículo en Inglés | MEDLINE | ID: mdl-29290336

10.

Predicting the effects of SNPs on transcription factor binding affinity.

Nishizaki, Sierra S; Ng, Natalie; Dong, Shengcheng; Porter, Robert S; Morterud, Cody; Williams, Colten; Asman, Courtney; Switzenberg, Jessica A; Boyle, Alan P.

Bioinformatics; 36(2): 364-372, 2020 01 15.

Artículo en Inglés | MEDLINE | ID: mdl-31373606

11.

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony.

Diehl, Adam G; Boyle, Alan P.

BMC Bioinformatics; 21(1): 416, 2020 Sep 22.

Artículo en Inglés | MEDLINE | ID: mdl-32962625

12.

Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.

Nishizaki, Sierra S; Boyle, Alan P.

Trends Genet; 33(1): 34-45, 2017 01.

Artículo en Inglés | MEDLINE | ID: mdl-27939749

13.

Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

Araya, Carlos L; Kawli, Trupti; Kundaje, Anshul; Jiang, Lixia; Wu, Beijing; Vafeados, Dionne; Terrell, Robert; Weissdepp, Peter; Gevirtzman, Louis; Mace, Daniel; Niu, Wei; Boyle, Alan P; Xie, Dan; Ma, Lijia; Murray, John I; Reinke, Valerie; Waterston, Robert H; Snyder, Michael.

Nature; 512(7515): 400-5, 2014 Aug 28.

Artículo en Inglés | MEDLINE | ID: mdl-25164749

14.

Principles of regulatory information conservation between mouse and human.

Cheng, Yong; Ma, Zhihai; Kim, Bong-Hyun; Wu, Weisheng; Cayting, Philip; Boyle, Alan P; Sundaram, Vasavi; Xing, Xiaoyun; Dogan, Nergiz; Li, Jingjing; Euskirchen, Ghia; Lin, Shin; Lin, Yiing; Visel, Axel; Kawli, Trupti; Yang, Xinqiong; Patacsil, Dorrelyn; Keller, Cheryl A; Giardine, Belinda; Kundaje, Anshul; Wang, Ting; Pennacchio, Len A; Weng, Zhiping; Hardison, Ross C; Snyder, Michael P.

Nature; 515(7527): 371-375, 2014 Nov 20.

Artículo en Inglés | MEDLINE | ID: mdl-25409826

15.

Comparative analysis of regulatory information and circuits across distant species.

Boyle, Alan P; Araya, Carlos L; Brdlik, Cathleen; Cayting, Philip; Cheng, Chao; Cheng, Yong; Gardner, Kathryn; Hillier, LaDeana W; Janette, Judith; Jiang, Lixia; Kasper, Dionna; Kawli, Trupti; Kheradpour, Pouya; Kundaje, Anshul; Li, Jingyi Jessica; Ma, Lijia; Niu, Wei; Rehm, E Jay; Rozowsky, Joel; Slattery, Matthew; Spokony, Rebecca; Terrell, Robert; Vafeados, Dionne; Wang, Daifeng; Weisdepp, Peter; Wu, Yi-Chieh; Xie, Dan; Yan, Koon-Kiu; Feingold, Elise A; Good, Peter J; Pazin, Michael J; Huang, Haiyan; Bickel, Peter J; Brenner, Steven E; Reinke, Valerie; Waterston, Robert H; Gerstein, Mark; White, Kevin P; Kellis, Manolis; Snyder, Michael.

Nature; 512(7515): 453-6, 2014 Aug 28.

Artículo en Inglés | MEDLINE | ID: mdl-25164757

16.

Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.

Diehl, Adam G; Boyle, Alan P.

Nucleic Acids Res; 46(4): 1878-1894, 2018 02 28.

Artículo en Inglés | MEDLINE | ID: mdl-29361190

17.

Predicting functional variants in enhancer and promoter elements using RegulomeDB.

Dong, Shengcheng; Boyle, Alan P.

Hum Mutat; 40(9): 1292-1298, 2019 09.

Artículo en Inglés | MEDLINE | ID: mdl-31228310

18.

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.

Shigaki, Dustin; Adato, Orit; Adhikari, Aashish N; Dong, Shengcheng; Hawkins-Hooker, Alex; Inoue, Fumitaka; Juven-Gershon, Tamar; Kenlay, Henry; Martin, Beth; Patra, Ayoti; Penzar, Dmitry D; Schubach, Max; Xiong, Chenling; Yan, Zhongxia; Boyle, Alan P; Kreimer, Anat; Kulakovskiy, Ivan V; Reid, John; Unger, Ron; Yosef, Nir; Shendure, Jay; Ahituv, Nadav; Kircher, Martin; Beer, Michael A.

Hum Mutat; 40(9): 1280-1291, 2019 09.

Artículo en Inglés | MEDLINE | ID: mdl-31106481

19.

Deciphering ENCODE.

Diehl, Adam G; Boyle, Alan P.

Trends Genet; 32(4): 238-249, 2016 Apr.

Artículo en Inglés | MEDLINE | ID: mdl-26962025

20.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein, Mark B; Kundaje, Anshul; Hariharan, Manoj; Landt, Stephen G; Yan, Koon-Kiu; Cheng, Chao; Mu, Xinmeng Jasmine; Khurana, Ekta; Rozowsky, Joel; Alexander, Roger; Min, Renqiang; Alves, Pedro; Abyzov, Alexej; Addleman, Nick; Bhardwaj, Nitin; Boyle, Alan P; Cayting, Philip; Charos, Alexandra; Chen, David Z; Cheng, Yong; Clarke, Declan; Eastman, Catharine; Euskirchen, Ghia; Frietze, Seth; Fu, Yao; Gertz, Jason; Grubert, Fabian; Harmanci, Arif; Jain, Preti; Kasowski, Maya; Lacroute, Phil; Leng, Jing Jane; Lian, Jin; Monahan, Hannah; O'Geen, Henriette; Ouyang, Zhengqing; Partridge, E Christopher; Patacsil, Dorrelyn; Pauli, Florencia; Raha, Debasish; Ramirez, Lucia; Reddy, Timothy E; Reed, Brian; Shi, Minyi; Slifer, Teri; Wang, Jing; Wu, Linfeng; Yang, Xinqiong; Yip, Kevin Y; Zilberman-Schapira, Gili.

Nature; 489(7414): 91-100, 2012 Sep 06.

Artículo en Inglés | MEDLINE | ID: mdl-22955619

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Dynamic trans-acting factor colocalization in human cells.

Personal omics profiling reveals dynamic molecular and medical phenotypes.

Multiplexed long-read plasmid validation and analysis using OnRamp.

Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome.

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence.

High-resolution mapping and characterization of open chromatin across the genome.

Broad noncoding transcription suggests genome surveillance by RNA polymerase V.

SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.

Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development.

Predicting the effects of SNPs on transcription factor binding affinity.

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony.

Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms.

Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

Principles of regulatory information conservation between mouse and human.

Comparative analysis of regulatory information and circuits across distant species.

Conserved and species-specific transcription factor co-binding patterns drive divergent gene regulation in human and mouse.

Predicting functional variants in enhancer and promoter elements using RegulomeDB.

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.

Deciphering ENCODE.

Architecture of the human regulatory network derived from ENCODE data.